Arun Seetharam
@arnstrm.bsky.social
Lead Bioinformatics Scientist @ RCAC, Purdue University| Genomics, Data Science, and Computational Biology | Empowering research with innovative solutions | Let’s connect for collaborations in life sciences and beyond!
Pinned
Arun Seetharam
@arnstrm.bsky.social
· Nov 19
🌽 "Kernel of Insight" 🌽
A starter pack of maize researchers to follow on Bluesky! Stay connected, share ideas, and grow your network in Zea mays science. 🌟
Suggestions welcome—let's build this community together!
#MaizeResearch #ZeaMays #KernelOfInsight
go.bsky.app/RPeENJz
A starter pack of maize researchers to follow on Bluesky! Stay connected, share ideas, and grow your network in Zea mays science. 🌟
Suggestions welcome—let's build this community together!
#MaizeResearch #ZeaMays #KernelOfInsight
go.bsky.app/RPeENJz
Reposted by Arun Seetharam
Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting:
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
March 7, 2025 at 2:39 AM
Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting:
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025
Reposted by Arun Seetharam
New preprint from @sjsnodgrass.bsky.social and our colleagues showing variable fractionation in Zea and Tripsacum post-polyploidy. We welcome your thoughts as we work toward submission to a journal.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Maize and wild relatives show distinct patterns of genome downsizing following polyploidy
Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, unt...
www.biorxiv.org
December 26, 2024 at 12:22 PM
New preprint from @sjsnodgrass.bsky.social and our colleagues showing variable fractionation in Zea and Tripsacum post-polyploidy. We welcome your thoughts as we work toward submission to a journal.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Arun Seetharam
The latest preprint from the PanAnd project, led by @mcstitzer.bsky.social is out today. We look at genome evolution in the Andropogoneae tribe of grasses. Interesting to see how processes occurring in #maize after #polyploidy may not be a general phenomenon.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 26, 2025 at 7:13 PM
The latest preprint from the PanAnd project, led by @mcstitzer.bsky.social is out today. We look at genome evolution in the Andropogoneae tribe of grasses. Interesting to see how processes occurring in #maize after #polyploidy may not be a general phenomenon.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Arun Seetharam
I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...
January 27, 2025 at 5:58 AM
I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...
Reposted by Arun Seetharam
New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...
January 27, 2025 at 9:33 PM
New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...
Reposted by Arun Seetharam
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...
December 16, 2024 at 9:25 AM
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...
Reposted by Arun Seetharam
I have written a couple of threads 🧵 on "classic" #PlantScience papers. I always tag them with #PlantScienceClassics , but will also compile them here in this thread: 👇
January 2, 2024 at 1:10 PM
I have written a couple of threads 🧵 on "classic" #PlantScience papers. I always tag them with #PlantScienceClassics , but will also compile them here in this thread: 👇
Reposted by Arun Seetharam
🎉I am really excited to share that our paper is out. We present PHILO ChIP-seq, a user-friendly and cost-effective platform for high-throughput, low-input chromatin profiling in plants!
From Mark Zander group
academic.oup.com/nar/advance-...
From Mark Zander group
academic.oup.com/nar/advance-...
December 8, 2024 at 5:40 AM
🎉I am really excited to share that our paper is out. We present PHILO ChIP-seq, a user-friendly and cost-effective platform for high-throughput, low-input chromatin profiling in plants!
From Mark Zander group
academic.oup.com/nar/advance-...
From Mark Zander group
academic.oup.com/nar/advance-...
Reposted by Arun Seetharam
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Redirecting
doi.org
December 2, 2024 at 4:44 PM
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Reposted by Arun Seetharam
Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations. https://www.biorxiv.org/content/10.1101/2024.12.06.627098v1
December 8, 2024 at 1:00 PM
Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations. https://www.biorxiv.org/content/10.1101/2024.12.06.627098v1
Reposted by Arun Seetharam
New insect genomes just dropped. Very happy to have been a (small) part of this cool project 😁
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis, Dyspersa pallida, and Trioza urticae (Hemiptera: Psylloidea)
Psyllids are major vectors of plant diseases, including Candidatus Liberibacter solanacearum (CLso), the bacterial agent associated with 'zebra chip' disease in potatoes and 'carrot yellows' disease i...
www.biorxiv.org
December 6, 2024 at 8:48 PM
New insect genomes just dropped. Very happy to have been a (small) part of this cool project 😁
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Arun Seetharam
Hey educators, tidyplots.org is great for teaching students data visualization because it is
🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful
#rstats #phd #dataviz #education
🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful
#rstats #phd #dataviz #education
December 6, 2024 at 8:36 PM
Hey educators, tidyplots.org is great for teaching students data visualization because it is
🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful
#rstats #phd #dataviz #education
🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful
#rstats #phd #dataviz #education
Reposted by Arun Seetharam
Cool preprint! How do polyploids lose genes during fractionation/diploidization? Old work in maize pointed to recombination-driven deletions (journals.plos.org/plosbiology/...) but generality was unclear. New evidence this is the more common deletion mechanism! www.researchsquare.com/article/rs-4...
The Subordinate Role of Pseudogenization over Recombinative Deletion Following Polyploidization in Angiosperms
Extensive gene loss is a key feature of the rediploidization process following polyploidization. Despites this, the molecular mechanisms behind such gene loss are unclear, whether it is through pseudo...
www.researchsquare.com
December 6, 2024 at 9:51 PM
Cool preprint! How do polyploids lose genes during fractionation/diploidization? Old work in maize pointed to recombination-driven deletions (journals.plos.org/plosbiology/...) but generality was unclear. New evidence this is the more common deletion mechanism! www.researchsquare.com/article/rs-4...
Reposted by Arun Seetharam
For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...
Hybrid adaptation is hampered by Haldane’s sieve - Nature Communications
Hybrids have complex genomes that influence their adaptive potential. This study reveals that yeast hybrids adapt slower than their parental species in a new environment, primarily due to a reduced ra...
www.nature.com
November 28, 2024 at 12:18 PM
For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...
Reposted by Arun Seetharam
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/dietvin/pod5...
December 5, 2024 at 2:07 PM
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/dietvin/pod5...
Reposted by Arun Seetharam
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning. #Nanopore #Sequencing #XenoNucleicAcids #XNAs #genomics #bioinformatics @nanoporetech.com 🧬🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 5, 2024 at 12:58 PM
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning. #Nanopore #Sequencing #XenoNucleicAcids #XNAs #genomics #bioinformatics @nanoporetech.com 🧬🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Arun Seetharam
🚨 Summer '25 Paid Internships! Join Purdue’s Anvil Research Experience for Undergraduates for hands-on experience in AI, bioinformatics, & data centers. $680/week + housing. Apply now: purdue.ca1.qualtrics.com/jfe/form/SV_... 🌟
Anvil REU Applications
Application submission for the Purdue Anvil REU program.
purdue.ca1.qualtrics.com
December 4, 2024 at 1:46 PM
🚨 Summer '25 Paid Internships! Join Purdue’s Anvil Research Experience for Undergraduates for hands-on experience in AI, bioinformatics, & data centers. $680/week + housing. Apply now: purdue.ca1.qualtrics.com/jfe/form/SV_... 🌟
Reposted by Arun Seetharam
Want to learn about the evolution of brown algae as derived from 60 new genomes? Exciting results of the Phaeoexplorer project:
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate …
www.sciencedirect.com
November 23, 2024 at 10:54 AM
Want to learn about the evolution of brown algae as derived from 60 new genomes? Exciting results of the Phaeoexplorer project:
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Arun Seetharam
Thrilled to see this paper out! 🎉
We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.
We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.
November 24, 2024 at 10:30 AM
Thrilled to see this paper out! 🎉
We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.
We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.
Reposted by Arun Seetharam
Exciting news! The latest hifiasm release from Haoyu Cheng and Heng Li adds beta support for @nanoporetech.com simplex R10 reads. Initial results look very promising. 🚀
Check it out: github.com/chhylp123/hi...
Check it out: github.com/chhylp123/hi...
Release Hifiasm-0.21.0-r686 · chhylp123/hifiasm
Since Hifiasm-0.20.0 (r639):
New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below:
hifiasm -t64 --ont -o...
github.com
November 27, 2024 at 7:11 PM
Exciting news! The latest hifiasm release from Haoyu Cheng and Heng Li adds beta support for @nanoporetech.com simplex R10 reads. Initial results look very promising. 🚀
Check it out: github.com/chhylp123/hi...
Check it out: github.com/chhylp123/hi...
Reposted by Arun Seetharam
If you've missed hyper-k-mers, this joint work with Lucas who's presenting, @imartayan.bsky.social Antoine Limasset and Yoshihiro Shibuya.
They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.
They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.
November 28, 2024 at 10:58 AM
If you've missed hyper-k-mers, this joint work with Lucas who's presenting, @imartayan.bsky.social Antoine Limasset and Yoshihiro Shibuya.
They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.
They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.
Reposted by Arun Seetharam
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them.
Read more: nanoporetech.com/news/oxford-...
Read more: nanoporetech.com/news/oxford-...
November 27, 2024 at 9:16 AM
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them.
Read more: nanoporetech.com/news/oxford-...
Read more: nanoporetech.com/news/oxford-...
Reposted by Arun Seetharam
bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis https://www.biorxiv.org/content/10.1101/2023.09.15.558026v2 🧬🖥️🧪 #rstats https://github.com/trichelab/bamSliceR from @timtriche.bsky.social lab
November 26, 2024 at 9:00 PM
bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis https://www.biorxiv.org/content/10.1101/2023.09.15.558026v2 🧬🖥️🧪 #rstats https://github.com/trichelab/bamSliceR from @timtriche.bsky.social lab
annoy a bioinformatician with these simple phrases:
"Can't you just use Excel?"
"Isn't BLAST basically Google for DNA?"
"But did you annotate it?"
"Can't you just use Excel?"
"Isn't BLAST basically Google for DNA?"
"But did you annotate it?"
November 26, 2024 at 11:23 PM
annoy a bioinformatician with these simple phrases:
"Can't you just use Excel?"
"Isn't BLAST basically Google for DNA?"
"But did you annotate it?"
"Can't you just use Excel?"
"Isn't BLAST basically Google for DNA?"
"But did you annotate it?"
Reposted by Arun Seetharam
Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience
@uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...
@uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...
November 26, 2024 at 10:19 PM
Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience
@uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...
@uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...